I am wondering about the best way to screen bacterial genomes for signs of horizontal gene transfers.
In particular, is there a database of website that could screen a genome and tag sequences that are homologous to that of temperate bacteriophages or transposons?
I suppose that I could do it individually by retrieving genomes of known mobile element and then blasting them one by one, but that seems terribly time consuming, especially if I am not familiar with the bacteriophages described in a given bacterial species.
I was wondering if there was a database that could ease such a job?
Not for transposons, but PHASTER ( https://phaster.ca/ ) is really good finding temperate phages.
ISfinder is usefull for finding insertion sequences but in most bacterial genomes there are usually too many.
Dear Simon Menanteau-Ledouble ,
I frequently use PHASTER ( https://phaster.ca/ ), and ProphET Article ProphET, prophage estimation tool: A stand-alone prophage se...
For transposon sequences, I use: https://isfinder.biotoul.fr/